TreeTime
Time-tree inference

Features

  • Maximum-likelihood time-scaled phylogenies
  • Inference of GTR models
  • Rerooting to obtain best root-to-tip regression
  • Coalescent priors

Requires

  • Alignment as fasta
  • Tip dates as csv
  • Tree as newick (optional)
Ancestral state reconstruction

Features

  • Ancestral sequence reconstruction
  • Branch length optimization
  • Inference of GTR models

Requires

  • Alignment as fasta
  • Tree as newick (optional)